* using log directory ‘/srv/hornik/tmp/CRAN_pretest/geneExpressionFromGEO.Rcheck’
* using R Under development (unstable) (2025-04-08 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (1+b1)
    Debian flang-new version 19.1.7 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘geneExpressionFromGEO/DESCRIPTION’ ... OK
* this is package ‘geneExpressionFromGEO’ version ‘1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/6s] OK
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘geneExpressionFromGEO’ can be installed ... [1s/1s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/8s] ERROR
Running examples in ‘geneExpressionFromGEO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getGeneExpressionFromGEO
> ### Title: Function that reads in the GEO code of a dataset, and returns
> ###   the gene expression dataframe.
> ### Aliases: getGeneExpressionFromGEO
> 
> ### ** Examples
> 
> geneExpressionDF1 <- getGeneExpressionFromGEO("GSE3268", FALSE, FALSE)
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/
Processed URL: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE3nnn/GSE3268
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Found 1 file(s)
GSE3268_series_matrix.txt.gz
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Failure when receiving data from the peer [ftp.ncbi.nlm.nih.gov]: GnuTLS recv error (-9): Error decoding the received TLS packet.File stored at:
/tmp/Rtmp89I4Zk/working_dir/Rtmpcr7Cs0/GSE3268_series_matrix.txt.gz
Error in downloadFile(url, destfile = destfile, mode = "wb") : 
  Failed to download /tmp/Rtmp89I4Zk/working_dir/Rtmpcr7Cs0/GSE3268_series_matrix.txt.gz!
Calls: getGeneExpressionFromGEO ... <Anonymous> -> getAndParseGSEMatrices -> downloadFile
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR